Package ffx.numerics.estimator
Class EstimateBootstrapper
java.lang.Object
ffx.numerics.estimator.EstimateBootstrapper
Bootstrap Free Energy Estimate.
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
bootstrap
(long trials) Perform bootstrap analysis.void
bootstrap
(long trials, long logInterval) Perform bootstrap analysis.static int[]
getBootstrapIndices
(int length) Gets randomized bootstrap indices; ensures there are at least two distinct indices.static int[]
getBootstrapIndices
(int length, Random random) Gets randomized bootstrap indices; ensures there are at least two distinct indices.static int[]
getBootstrapIndices
(int length, Random random, int minDistinct) Gets randomized bootstrap indices; ensures there are at least a few distinct indices.double[]
Get bootstrap enthalpy estimate for each window.Get bootstrap Enthalpy results for each window.double[]
Get the enthalpy standard deviation estimate from bootstrap analysis for each window.double[]
Get the enthalpy variance estimate from bootstrap analysis for each window.double[]
Get bootstrap entropy estimate for each window (-TdS).double[]
Get the entropy standard deviation estimate from bootstrap analysis for each window.double[]
Get the free energy difference uncertainties (standard deviations) from bootstrap analysis for each window.double[]
Get the free energy difference variance estimate from bootstrap analysis for each window.double[]
Get bootstrap free energy estimate for each window.double
Get the total enthalpy estimate from bootstrap analysis.double
getTotalEnthalpyChange
(double[] enthalpyChanges) Get the total enthalpy estimate from per window bootstrap analysis.double
Get the total enthalpy uncertainty estimate from bootstrap analysis.double
getTotalEnthalpyUncertainty
(double[] variances) Get the total enthalpy uncertainty estimate from per window bootstrap analysis.double
Get the total entropy change (-TdS) from bootstrap analysis.double
Get the total entropy uncertainty estimate from bootstrap analysis.double
Get the total free energy difference uncertainty estimate from bootstrap analysis.double
getTotalFEDifferenceUncertainty
(double[] variances) Get the total free energy difference uncertainty estimate from per window bootstrap analysis.double
Get the total free energy difference estimate from bootstrap analysis.double
getTotalFreeEnergyDifference
(double[] freeEnergyDifferences) Get the total free energy difference estimate from per window bootstrap analysis.
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Constructor Details
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EstimateBootstrapper
Constructor.- Parameters:
estimator
- Estimator to bootstrap.
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Method Details
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getBootstrapIndices
public static int[] getBootstrapIndices(int length) Gets randomized bootstrap indices; ensures there are at least two distinct indices.- Parameters:
length
- Number of random indices to generate in range [0,length)- Returns:
- Randomized indices.
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getBootstrapIndices
Gets randomized bootstrap indices; ensures there are at least two distinct indices.- Parameters:
length
- Number of random indices to generate in range [0,length)random
- Source of randomness.- Returns:
- Randomized indices.
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getBootstrapIndices
Gets randomized bootstrap indices; ensures there are at least a few distinct indices.- Parameters:
length
- Number of random indices to generate in range [0,length)random
- Source of randomness.minDistinct
- Minimum number of distinct indices.- Returns:
- Randomized indices.
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getEnthalpyResults
Get bootstrap Enthalpy results for each window.- Returns:
- Bootstrap Enthalpy results for each window.
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bootstrap
public void bootstrap(long trials) Perform bootstrap analysis.- Parameters:
trials
- Number of trials.
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bootstrap
public void bootstrap(long trials, long logInterval) Perform bootstrap analysis.- Parameters:
trials
- Number of trials.logInterval
- Interval between logging statements.
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getTotalFreeEnergyDifference
public double getTotalFreeEnergyDifference()Get the total free energy difference estimate from bootstrap analysis.- Returns:
- The total free energy difference estimate.
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getTotalEnthalpyChange
public double getTotalEnthalpyChange()Get the total enthalpy estimate from bootstrap analysis.- Returns:
- The total enthalpy estimate.
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getTotalEntropyChange
public double getTotalEntropyChange()Get the total entropy change (-TdS) from bootstrap analysis.- Returns:
- The total entropy change (-TdS).
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getFreeEnergyDifferences
public double[] getFreeEnergyDifferences()Get bootstrap free energy estimate for each window.getFreeEnergyDifferences
- Returns:
- Return the bootstrap free energy difference estimate for each window.
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getEnthalpyChanges
public double[] getEnthalpyChanges()Get bootstrap enthalpy estimate for each window.- Returns:
- Return the bootstrap enthalpy estimate for each window.
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getEntropyChanges
public double[] getEntropyChanges()Get bootstrap entropy estimate for each window (-TdS).- Returns:
- Return the bootstrap entropy estimate (-TdS) for each window.
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getTotalFEDifferenceUncertainty
public double getTotalFEDifferenceUncertainty()Get the total free energy difference uncertainty estimate from bootstrap analysis.- Returns:
- The total free energy difference uncertainty estimate.
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getTotalEnthalpyUncertainty
public double getTotalEnthalpyUncertainty()Get the total enthalpy uncertainty estimate from bootstrap analysis.- Returns:
- The total enthalpy uncertainty estimate.
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getTotalEntropyUncertainty
public double getTotalEntropyUncertainty()Get the total entropy uncertainty estimate from bootstrap analysis. This is computed as the sqrt of the sum of the free energy and enthalpy variances.- Returns:
- The total enthalpy uncertainty estimate.
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getFEDifferenceStdDevs
public double[] getFEDifferenceStdDevs()Get the free energy difference uncertainties (standard deviations) from bootstrap analysis for each window.- Returns:
- Returns free energy difference standard deviation estimate for each window.
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getEnthalpyStdDevs
public double[] getEnthalpyStdDevs()Get the enthalpy standard deviation estimate from bootstrap analysis for each window.- Returns:
- Returns enthalpy standard deviation estimate for each window.
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getEntropyStdDevs
public double[] getEntropyStdDevs()Get the entropy standard deviation estimate from bootstrap analysis for each window.This is computed as the sqrt of the sum of the free energy and enthalpy variances for each window.
- Returns:
- Returns enthalpy standard deviation estimate for each window.
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getTotalFreeEnergyDifference
public double getTotalFreeEnergyDifference(double[] freeEnergyDifferences) Get the total free energy difference estimate from per window bootstrap analysis.- Parameters:
freeEnergyDifferences
- The free energy difference estimate for each window.- Returns:
- The total free energy difference estimate from bootstrap analysis.
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getFEDifferenceVariances
public double[] getFEDifferenceVariances()Get the free energy difference variance estimate from bootstrap analysis for each window.- Returns:
- Returns free energy difference variance estimate for each window.
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getTotalFEDifferenceUncertainty
public double getTotalFEDifferenceUncertainty(double[] variances) Get the total free energy difference uncertainty estimate from per window bootstrap analysis.- Parameters:
variances
- The free energy difference variance estimate (not uncertainty) for each window.- Returns:
- The total free energy difference uncertainty from bootstrap analysis.
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getTotalEnthalpyChange
public double getTotalEnthalpyChange(double[] enthalpyChanges) Get the total enthalpy estimate from per window bootstrap analysis.- Parameters:
enthalpyChanges
- The enthalpy estimate for each window.- Returns:
- The total enthalpy difference estimate from bootstrap analysis.
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getTotalEnthalpyUncertainty
public double getTotalEnthalpyUncertainty(double[] variances) Get the total enthalpy uncertainty estimate from per window bootstrap analysis.- Parameters:
variances
- The enthalpy variance estimate (not uncertainty) for each window.- Returns:
- The total enthalpy uncertainty estimate from bootstrap analysis.
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getEnthalpyVariances
public double[] getEnthalpyVariances()Get the enthalpy variance estimate from bootstrap analysis for each window.- Returns:
- Returns enthalpy variance estimate for each window.
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